Pixel size to design to to allow for menu bars

I designed an interactive ipad. I made it to the ipad size, 768x1024. When I open it in Acrobat on my ipad, there is a bunch of text cut off because of the Acrobat menu bar in continuous. Should I design it to 768x1024 or reduce the size of the page, so that my text isn't cut off and I'm allowing for the menu bar at top/bottom? I don't know if the viewer will be in continuous or single page. I just want the hot spots at the bottom to show up in every view.

Thx!